Workflows used for QC of WGS data

Whole Genome Single Sample QC :

This WDL pipeline implements QC in human whole-genome sequencing data.


  • Human whole-genome paired-end sequencing data in aligned BAM or CRAM format
  • Input BAM/CRAM files must additionally comply with the following requirements:
    • files must pass validation by ValidateSamFile
    • reads are provided in query-sorted order
    • all reads must have an RG tag
  • Reference gen

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